You can feel free to PM me about anything specific if you'd like. I can't be a tour guide for you because I moved to Atlanta, GA, USA, but again, since I lived in Japan for 3 years and just left in September, I know a lot of things.
I honestly would suggest using trains to get around. They're reasonably priced, clean, and are exactly on time 99% of the time. You can use this site to find out the train schedules. You have to know the names of the closest station to where you want to go, but if you do a search on Google for things you want to visit, pretty much every Japanese store/location you might want to visit has an "Access" page and it will tell you the name of the closest train station.
http://www.hyperdia.com/en/
Keep in mind that Kyoto isn't as good for trains. You can get to Kyoto with trains, and it does have a limited subway system. But most of Kyoto you'll have to walk or use buses to get around. Tokyo and Osaka you can get around everywhere with trains though.
Some particular things I'd recommend going to see:
Osaka:
- Nipponbashi (sometimes called Den Den Town). This is like Osaka's version of Akihabara. It's very different from Akihabara. Less crowded, different things available. I specifically recommend you visit
Jungle if you want to see a giant store full of all kinds of anime, video game, etc goodies. Jungle is in Akihabara too, but their best store is in Osaka's Nipponbashi.
- Kaiyukan (Osaka Aquarium). This is one of the few places in the world you can see a whale shark. This place is really cool. There's also a giant ferris wheel nearby called the Tempozan and a small mall + food court that has interesting things.
http://www.kaiyukan.com/language/eng/
If you have girls in your group and you like Alice in Wonderland themed stuff, I specifically recommend trying to visit Alice on Wednesday. Most non-Japanese don't know about this shop. There's one in Tokyo and one in Osaka. I recommend going on a weekday and getting there shortly before the store opens. There may be someone passing out entry tickets with a time for entry, and there may be an entry line. The ladies at Alice on Wednesday don't seem to speak much English, but they're very good at directing you where you need to go. The Osaka store is right next to Jungle in Nipponbashi, the Tokyo store is in a part of Tokyo called Harajuku. The Osaka one is easiest of the two to find if you're not with a person who doesn't speak Japanese.
http://www.aliceonwednesday.jp/
There's tons to see in Kyoto. It really depends on what your particular priorities are. Try to see some old temples and shrines, hopefully you can see a maiko. If you see a maiko going about her job, you'll probably see tourists taking lots of pictures of her. Don't do this. It's actually considered rude. I would suggest standing out of her way and quietly admiring her kimono from a distance.
For Tokyo, don't just go to Akihabara if you're all anime fans. I highly suggest you going to the other side of Tokyo at some point and visiting Nakano Broadway. Akihabara mostly has stuff for the latest and greatest anime that have come out in the past few years. Nakano Broadway has a lot of things for older anime. Here's some info about Nakano Broadway.
http://www.nbw.jp/index_e.html I don't know what hotel you'll be staying in while you're in Tokyo, but if you use that Hyperdia site I linked above, you would plug in the name of the train station closest to your hotel and then put NAKANO as the ending train station.
